Nothing
R/meta-internal.R
In meta: General Package for Meta-Analysis
Defines functions
second
setVar
getVar
setOption
catobsev
cathet
condense
collapse
qdat
hetdat
taudat
update_needed
updateversion
.onAttach
.onAttach <- function(libname, pkgname) {
msg <-
paste0("Loading 'meta' package (version ",
utils::packageDescription("meta")$Version,
").",
"\nType 'help(meta)' for a brief overview.")
packageStartupMessage(msg)
}
updateversion <- function(x) {
##
## Update older meta objects, see gs("major.update") and gs("minor.update")
##
if (update_needed(x$version))
x <- update(x, warn = FALSE, warn.deprecated = FALSE)
##
x
}
update_needed <- function(version,
major = gs("major.update"),
minor = gs("minor.update"),
verbose = FALSE) {
if (is.null(version)) {
version <- 0.1
major.cur <- 0
minor.cur <- 1
}
else {
version <- unlist(strsplit(version, "-"))
divide <- unlist(strsplit(version[1], ".", fixed = TRUE))
major.cur <- as.numeric(divide[1])
minor.cur <- as.numeric(paste(divide[2], version[2], sep = "."))
}
##
res <-
ifelse(major.cur < major,
TRUE, ifelse(major.cur > major,
FALSE, minor.cur < as.numeric(gsub("-", ".", minor))))
if (res & verbose)
message(paste0("Update to meta, version ", major, ".", minor))
##
res
}
taudat <- function(method.tau, detail.tau,
tau, lower.tau, upper.tau, print.tau.ci, digits.tau,
tau2, lower.tau2, upper.tau2, print.tau2.ci, digits.tau2,
sign.lower, sign.upper) {
dat <- data.frame(method.tau, names = detail.tau, tau, tau2)
##
## In order to use duplicated()
##
if (!is.null(dat$tau))
dat$tau <- round(dat$tau, 14)
if (!is.null(dat$tau2))
dat$tau2 <- round(dat$tau2, 14)
##
if (!is.null(lower.tau))
dat$lower.tau <- round(lower.tau, 14)
if (!is.null(lower.tau2))
dat$lower.tau2 <- round(lower.tau2, 14)
##
if (!is.null(upper.tau))
dat$upper.tau <- round(upper.tau, 14)
if (!is.null(upper.tau2))
dat$upper.tau2 <- round(upper.tau2, 14)
##
if (!is.null(sign.lower))
dat$sign.lower <- sign.lower
if (!is.null(sign.upper))
dat$sign.upper <- sign.upper
##
if (!is.null(names(tau)))
dat$names <- names(tau)
##
sel1 <- !duplicated(dat[, c("method.tau", "tau", "tau2")])
##
if (!is.null(dat$lower.tau) & !is.null(dat$lower.tau2) &
!is.null(dat$upper.tau) & !is.null(dat$upper.tau2))
sel2 <- !duplicated(dat[, c("method.tau", "tau", "tau2",
"lower.tau", "upper.tau",
"lower.tau2", "upper.tau2")])
else
sel2 <- sel1
##
sel <- sel1 & sel2
##
dat <- dat[sel, , drop = FALSE]
##
if (print.tau.ci) {
dat$lower.tau <- round(dat$lower.tau, digits.tau)
dat$upper.tau <- round(dat$upper.tau, digits.tau)
}
##
if (print.tau2.ci) {
dat$lower.tau2 <- round(dat$lower.tau2, digits.tau2)
dat$upper.tau2 <- round(dat$upper.tau2, digits.tau2)
}
dat
}
hetdat <- function(I2, lowI2, uppI2, print.I2, print.I2.ci, digits.I2,
H, lowH, uppH, print.H, digits.H,
Rb, lowRb, uppRb, print.Rb) {
dat <- data.frame()
##
if (print.I2) {
if (nrow(dat) == 0)
dat <- data.frame(I2 = round(I2, digits.I2))
else
dat$I2 <- round(I2, digits.I2)
##
if (print.I2.ci) {
dat$lowI2 <- round(lowI2, digits.I2)
dat$uppI2 <- round(uppI2, digits.I2)
}
}
##
if (print.H) {
if (nrow(dat) == 0)
dat <- data.frame(H = round(H, digits.H))
else
dat$H <- round(H, digits.H)
##
if (print.I2.ci) {
dat$lowH <- round(lowH, digits.H)
dat$uppH <- round(uppH, digits.H)
}
}
##
if (print.Rb) {
if (nrow(dat) == 0)
dat <- data.frame(Rb = round(Rb, digits.I2))
else
dat$Rb <- round(Rb, digits.I2)
##
if (print.I2.ci) {
dat$lowRb <- round(lowRb, digits.I2)
dat$uppRb <- round(uppRb, digits.I2)
}
}
##
if (!is.null(names(I2)))
dat$names <- names(I2)
else if (!is.null(names(H)))
dat$names <- names(H)
else if (!is.null(names(Rb)))
dat$names <- names(Rb)
##
dat <- unique(dat)
dat
}
qdat <- function(Q, df.Q, pval.Q, hetlabel, text.common) {
if (length(Q) > 1) {
if (!is.null(names(Q)))
rownames.Q <- names(Q)
else if (!is.null(hetlabel) && length(hetlabel) == length(Q))
rownames.Q <- hetlabel
else if (length(text.common) == length(Q))
rownames.Q <- text.common
else
rownames.Q <- rep("", length(Q))
}
else
rownames.Q <- rep("", length(Q))
##
sel <- rownames.Q != ""
rownames.Q[sel] <- paste0(" ", rownames.Q[sel])
##
dat <- data.frame(Q, df.Q, pval.Q, names = rownames.Q)
dat <- unique(dat)
dat
}
collapse <- function(x, quote = '"', collapse = ", ", sort = FALSE)
paste0(paste0(quote, if (sort) sort(x) else x, quote, collapse = collapse))
condense <- function(x, var)
unlist(lapply(x, "[[" , var))
cathet <- function(k,
method.tau, detail.tau,
tau2, lower.tau2, upper.tau2,
print.tau2, print.tau2.ci, text.tau2, digits.tau2,
tau, lower.tau, upper.tau,
print.tau, print.tau.ci, text.tau, digits.tau,
sign.lower.tau, sign.upper.tau,
I2, lowI2, uppI2,
print.I2, print.I2.ci, text.I2, digits.I2,
H, lowH, uppH,
print.H, digits.H,
Rb, lowRb, uppRb,
print.Rb, text.Rb,
big.mark,
sort.tau = NULL, sort.het = NULL) {
if (is.null(lower.tau2))
lower.tau2 <- NA
if (is.null(upper.tau2))
upper.tau2 <- NA
if (is.null(lower.tau))
lower.tau <- NA
if (is.null(upper.tau))
upper.tau <- NA
##
if (all(is.na(lower.tau2) & is.na(upper.tau2)))
print.tau2.ci <- FALSE
if (all(is.na(lower.tau) & all(is.na(upper.tau))))
print.tau.ci <- FALSE
## Text for tau2 and tau
##
dtau <- taudat(method.tau, detail.tau,
tau, lower.tau, upper.tau, print.tau.ci, digits.tau,
tau2, lower.tau2, upper.tau2, print.tau2.ci, digits.tau2,
sign.lower.tau, sign.upper.tau)
##
ntau <- nrow(dtau)
sort.tau <- setsort(sort.tau, ntau, "tau2 estimates")
dtau <- dtau[sort.tau, , drop = FALSE]
##
if (print.tau2 | print.tau) {
if (ntau > 1) {
text.tau2 <- paste(text.tau2, seq_len(ntau), sep = ".")
text.tau <- paste(text.tau, seq_len(ntau), sep = ".")
}
}
##
label.tau <-
if (ntau > 1)
ifelse(dtau$names == "", "", paste0(" (", dtau$names, ")"))
else
""
##
if (print.tau2.ci) {
text.tau2.ci <-
pasteCI(dtau$lower.tau2, dtau$upper.tau2,
digits.tau2, big.mark,
dtau$sign.lower, dtau$sign.upper)
text.tau2.ci[text.tau2.ci == " "] <- ""
}
else
text.tau2.ci <- ""
##
if (print.tau.ci) {
text.tau.ci <-
pasteCI(dtau$lower.tau, dtau$upper.tau,
digits.tau, big.mark,
dtau$sign.lower, dtau$sign.upper)
text.tau.ci[text.tau.ci == " "] <- ""
}
else
text.tau.ci <- ""
##
hettxt <-
paste0(
if (print.tau2 | print.tau | print.I2 | print.H | print.Rb)
" ",
if (print.tau2)
paste0(formatPT(dtau$tau2,
lab = TRUE, labval = text.tau2,
digits = digits.tau2,
lab.NA = "NA",
big.mark = big.mark),
text.tau2.ci,
if (!print.tau) label.tau),
##
if (print.tau)
paste0(
if (print.tau2) "; " else "",
formatPT(dtau$tau,
lab = TRUE, labval = text.tau,
digits = digits.tau,
lab.NA = "NA",
big.mark = big.mark),
text.tau.ci,
label.tau),
collapse = "\n")
## Text for I2, H and Rb
##
dhet <- hetdat(I2, lowI2, uppI2, print.I2, print.I2.ci, digits.I2,
H, lowH, uppH, print.H, digits.H,
Rb, lowRb, uppRb, print.Rb)
##
nhet <- nrow(dhet)
sort.het <- setsort(sort.het, nhet, "heterogeneity estimates")
dhet <- dhet[sort.het, , drop = FALSE]
##
label.het <-
if (nhet > 1)
ifelse(dhet$names == "", "", paste0(" (", dhet$names, ")"))
else
""
##
if (print.I2) {
if (nhet > 1)
text.I2 <- paste(text.I2, seq_len(nhet), sep = ".")
}
##
if (print.H) {
text.H <- "H"
if (nhet > 1)
text.H <- paste(text.H, seq_len(nhet), sep = ".")
}
##
if (print.Rb) {
if (nhet > 1)
text.Rb <- paste(text.Rb, seq_len(nhet), sep = ".")
}
##
if (print.I2)
hettxt <-
paste0(hettxt,
ifelse(print.tau2 | print.tau,
ifelse(ntau > 1 | print.tau2.ci | print.tau.ci |
(options()$width < 70 & print.I2.ci),
"\n", ";"),
""))
##
hettxt <-
paste0(hettxt,
paste0(
if (print.I2)
paste0(
if (print.tau2 | print.tau)
" ",
text.I2, " = ",
ifelse(is.na(dhet$I2), "NA",
paste0(formatN(dhet$I2, digits.I2), "%")),
if (print.I2.ci)
pasteCI(dhet$lowI2, dhet$uppI2, digits.I2,
big.mark, unit = "%"),
if (nhet > 1 & !print.H)
label.het
),
##
if (print.H)
paste0(
if (print.tau2 | print.tau | print.I2)
"; " else " ",
text.H, " = ",
ifelse(is.na(dhet$H), "NA",
formatN(dhet$H, digits.H, "NA", big.mark = big.mark)),
if (print.I2.ci & any(!is.na(lowH) & !is.na(uppH)))
pasteCI(dhet$lowH, dhet$uppH, digits.H, big.mark),
if (nhet > 1)
label.het),
collapse = "\n")
)
##
if (print.Rb)
hettxt <-
paste0(hettxt,
ifelse(print.tau2 | print.tau | print.I2 | print.H,
ifelse(ntau > 1 | nhet > 1 |
print.tau2.ci | print.tau.ci |
print.I2.ci |
(options()$width < 70 & print.I2.ci),
"\n", ";"),
""))
##
if (print.Rb)
hettxt <-
paste0(hettxt,
paste0(
" ",
text.Rb, " = ",
ifelse(is.na(dhet$Rb), "NA",
paste0(formatN(dhet$Rb, digits.I2,
big.mark = big.mark), "%")),
if (any(!is.na(dhet$lowRb) & !is.na(dhet$uppRb)))
pasteCI(dhet$lowRb, dhet$uppRb, digits.I2,
big.mark, unit = "%"),
label.het,
collapse = "\n")
)
## Remove spaces before ";", " (" and a line break
##
hettxt <- gsub("(*UCP)\\s+(;)", "\\1", hettxt, perl = TRUE)
hettxt <- gsub("(*UCP)\\s+( \\()", "\\1", hettxt, perl = TRUE)
hettxt <- gsub("(*UCP)\\s+(\\\n)", "\\1", hettxt, perl = TRUE)
## Print information on heterogeneity
##
cat(hettxt)
## Empty row(s)
##
if (print.tau2 | print.tau | print.I2 | print.H | print.Rb)
cat("\n")
invisible(NULL)
}
catobsev <- function(var1, var2 = NULL, type = "n", addrow = FALSE,
big.mark = gs("big.mark")) {
if (type == "n") {
txt <- "observations"
idx <- "o"
}
else if (type == "e") {
txt <- "events"
idx <- "e"
}
##
if (!is.null(var1) & !is.null(var2)) {
if (!(all(is.na(var1)) | all(is.na(var2)))) {
sum1 <- sum(var1, na.rm = TRUE)
sum2 <- sum(var2, na.rm = TRUE)
##
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum1 + sum2, big.mark = big.mark),
if (type == "n")
paste0(" (", idx, ".e = ",
format(sum1, big.mark = big.mark),
", ", idx, ".c = ",
format(sum2, big.mark = big.mark),
")"),
"\n"))
}
}
else if (!is.null(var1)) {
if (!all(is.na(var1))) {
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum(var1, na.rm = TRUE),
big.mark = big.mark),
"\n"))
}
}
else if (!is.null(var2)) {
if (!all(is.na(var2))) {
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum(var2, na.rm = TRUE), big.mark = big.mark),
"\n"))
}
}
##
if (addrow)
cat("\n")
##
invisible(NULL)
}
## The following R code is based on the file snowfall-internal.R from
## R package snowfall (Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>)
##
## Helpers for managing the internal variables in the package namespace without
## awake the R CMD check for later R versions (which basically blaims many
## global assignments).
##
## The given solution has an advantage: only writing is affected. Reading of the
## objects can remain the same (thanks to Uwe Ligges for the tipp):
## reading: gs("CIbracket")
## writing: setOption("CIbracket", "(")
##
##
## Set an option in the meta option list.
## (Basically this is the setting of a list entry).
## key - character: object name
## val - object (everything is allowed, even NULL)
##
setOption <- function(key = NULL, val = NULL) {
if(!is.null(key) && is.character(key)) {
option <- getVar(".settings") # Get from NS
option[[key]] <- val
setVar(".settings", option) # Write to NS
##
return(invisible(TRUE))
}
##
stop("Argument 'key' or 'val' is NULL or 'key' is no string.")
}
##
## Get a specific variable from the meta namespace.
## var - character: object name
##
getVar <- function(var = NULL) {
if(!is.null(var) && is.character(var)) {
tmp <- try(getFromNamespace(var, "meta"))
##
if(inherits(tmp, "try-error"))
stop("Object", var, "not found in meta package.")
##
return(tmp)
}
stop("Argument 'var' is NULL or not a string.")
}
##
## Write a specific variable to the meta namespace.
## var - character: object name
## arg - object (NULL allowed)
##
setVar <- function(var = NULL, arg = NULL) {
if(!is.null(var) && is.character(var)) {
assignInNamespace(var, arg, "meta")
return(invisible(TRUE))
}
stop("var is NULL or no character");
}
second <- function(x) x[2]
.settings <- list()
##
## List of internal settings
##
argslist.internal <-
c("Wan2014.Table1", "Wan2014.Table2",
"sm4bin", "sm4cont", "sm4cor", "sm4inc", "sm4mean", "sm4prop", "sm4rate",
"ci4cont", "ci4prop", "ci4rate",
"meth4bin", "meth4inc", "meth4prop", "meth4rate",
"meth4tau", "meth4tau.ci", "meth4i2",
"meth4random.ci", "meth4pi",
"adhoc4hakn.ci", "adhoc4hakn.pi",
"meth4bias", "meth4bias.old",
"tool4rob",
"meth4incr",
"text.fixed", "text.w.fixed",
"major.update", "minor.update",
#
"special.characters")
##
setOption("argslist.internal", argslist.internal)
##
## Set defaults (for internal options)
##
setOption("sm4bin", c("OR", "RD", "RR", "ASD", "DOR", "VE"))
setOption("sm4cont", c("MD", "SMD", "ROM"))
setOption("sm4cor", c("ZCOR", "COR"))
setOption("sm4inc", c("IRR", "IRD", "IRSD", "VE"))
setOption("sm4mean", c("MRAW", "MLN"))
setOption("sm4prop", c("PLOGIT", "PLN", "PRAW", "PAS", "PFT"))
setOption("sm4rate", c("IR", "IRLN", "IRS", "IRFT"))
##
setOption("ci4cont", c("z", "t"))
setOption("ci4prop", c("CP", "WS", "WSCC", "AC", "SA", "SACC", "NAsm"))
setOption("ci4rate", c("NAsm", "Poisson"))
##
setOption("meth4bin", c("Inverse", "MH", "Peto", "GLMM", "LRP", "SSW"))
setOption("meth4inc", c("Inverse", "MH", "Cochran", "GLMM"))
setOption("meth4prop", c("Inverse", "GLMM"))
setOption("meth4rate", c("Inverse", "GLMM"))
##
setOption("meth4tau", c("DL", "PM", "REML", "ML", "HS", "SJ", "HE", "EB"))
setOption("meth4tau.ci", c("QP", "BJ", "J", "PL", ""))
setOption("meth4i2", c("Q", "tau2"))
setOption("meth4random.ci", c("classic", "HK", "KR"))
setOption("meth4pi",
c("V", "HTS", "HK", "HK-PR", "KR", "KR-PR", "NNF", "S", ""))
setOption("adhoc4hakn.ci", c("", "se", "ci", "IQWiG6"))
setOption("adhoc4hakn.pi", c("", "se"))
##
setOption("meth4bias.old", c("rank", "linreg", "mm", "count", "score"))
setOption("meth4bias", c("Begg", "Egger", "Thompson", "Schwarzer",
"Harbord", "Peters", "Deeks",
"Pustejovsky", "Macaskill"))
##
setOption("tool4rob",
c("RoB1", "RoB2", "RoB2-cluster", "RoB2-crossover",
"ROBINS-I", "ROBINS-E"))
##
setOption("meth4incr", c("only0", "if0all", "all"))
#
setOption("special.characters", c("+", ".", "&", "$", "#", "|", "*", "^"))
#
setOption("major.update", 5)
setOption("minor.update", 6)
##
## List of arguments that can be changed by user
##
argslist <-
c("level", "level.ma", "common", "random",
"method.random.ci", "method.predict",
"adhoc.hakn.ci", "adhoc.hakn.pi",
"method.tau", "method.tau.ci", "level.hetstat", "tau.common",
"method.I2",
"prediction", "level.predict",
"method.bias",
"tool.rob",
"overall.hetstat",
"text.common", "text.random", "text.predict",
"text.w.common", "text.w.random",
"title", "complab",
"CIbracket", "CIseparator", "CIlower.blank", "CIupper.blank",
"print.subgroup.name", "sep.subgroup",
"keepdata", "keeprma", "warn", "warn.deprecated",
"transf", "backtransf",
"smbin", "smcont", "smcor", "sminc", "smmean", "smprop", "smrate",
"incr", "method.incr",
"method", "allstudies", "MH.exact",
"RR.Cochrane", "Q.Cochrane", "model.glmm", "print.CMH",
"pooledvar", "method.smd", "sd.glass", "exact.smd",
"method.ci.cont", "method.ci.prop", "method.ci.rate",
"label.e", "label.c", "label.left", "label.right",
"layout", "forest.details",
"test.overall", "test.subgroup", "prediction.subgroup",
"test.effect.subgroup",
"digits", "digits.mean", "digits.sd", "digits.se", "digits.stat",
"digits.Q", "digits.tau2", "digits.tau", "digits.H", "digits.I2",
"digits.prop", "digits.weight",
"digits.pval", "digits.pval.Q",
"digits.forest", "digits.TE.forest",
"digits.df",
"scientific.pval", "big.mark", "zero.pval", "JAMA.pval",
"details",
"print.tau2", "print.tau2.ci", "print.tau", "print.tau.ci",
"print.I2", "print.I2.ci", "print.H", "print.Rb",
"text.tau2", "text.tau", "text.I2", "text.Rb",
"print.Q",
##
"lty.common", "lty.random", "col.common", "col.random",
"sort.subgroup",
"pooled.events", "pooled.times", "study.results",
"lower.equi", "upper.equi", "lty.equi", "col.equi", "fill.equi",
"fill",
"leftcols", "rightcols", "leftlabs", "rightlabs",
"label.e.attach", "label.c.attach",
"bottom.lr",
"lab.NA", "lab.NA.effect", "lab.NA.weight",
"lwd", "lwd.square", "lwd.diamond",
"arrow.type", "arrow.length",
"type.study", "type.common",
"col.study", "col.square", "col.square.lines", "col.circle", "col.inside",
"col.diamond", "col.diamond.lines",
"col.predict", "col.predict.lines",
"col.subgroup",
"col.label.right", "col.label.left",
"col.lines", "col.label",
"hetlab", "resid.hetstat", "resid.hetlab",
"forest.I2", "forest.I2.ci", "forest.tau2", "forest.tau2.ci",
"forest.tau", "forest.tau.ci", "forest.Q", "forest.pval.Q",
"forest.Rb", "forest.Rb.ci",
"text.subgroup.nohet",
"LRT",
"forest.stat", "forest.Q.subgroup",
"header.line",
"fontsize", "fontfamily",
"fs.common", "fs.random", "fs.predict",
"fs.common.labels", "fs.random.labels", "fs.predict.labels",
"fs.hetstat", "fs.test.overall", "fs.test.subgroup",
"fs.test.effect.subgroup", "fs.addline",
"ff.heading", "ff.common", "ff.random", "ff.predict",
"ff.common.labels", "ff.random.labels", "ff.predict.labels",
"ff.study", "ff.hetstat", "ff.test.overall", "ff.test.subgroup",
"ff.test.effect.subgroup", "ff.addline",
"ff.axis", "ff.smlab", "ff.xlab", "ff.lr",
"colgap", "colgap.forest",
"width",
"calcwidth.predict", "calcwidth.hetstat",
"calcwidth.tests", "calcwidth.subgroup", "calcwidth.addline",
"just.studlab", "just.addcols",
"spacing",
"addrow", "addrow.overall", "addrow.subgroups", "addrows.below.overall"
)
#
args.depr <- c("fixed", "comb.fixed", "comb.random", "level.comb",
"hakn", "adhoc.hakn",
"digits.zval", "print.byvar", "byseparator",
"addincr", "allincr")
#
setOption("argslist", c(argslist, args.depr))
#
setOption("argslist.meta", c(argslist, args.depr))
##
## General settings
##
setOption("level", 0.95)
setOption("level.ma", 0.95)
setOption("level.comb", 0.95)
##
setOption("common", TRUE)
setOption("fixed", TRUE)
setOption("comb.fixed", TRUE)
setOption("random", TRUE)
setOption("comb.random", TRUE)
setOption("method.random.ci", "classic")
setOption("hakn", FALSE)
setOption("adhoc.hakn", "")
setOption("adhoc.hakn.ci", "")
setOption("adhoc.hakn.pi", "")
setOption("prediction", FALSE)
setOption("level.predict", 0.95)
setOption("method.predict", "V")
setOption("method.tau", "REML")
setOption("method.tau.ci", NULL)
setOption("level.hetstat", 0.95)
setOption("tau.common", FALSE)
setOption("method.I2", "Q")
setOption("method.bias", "Egger")
setOption("tool.rob", NULL)
setOption("overall.hetstat", NULL)
setOption("text.common", "Common effect model")
setOption("text.fixed", "Common effect model")
setOption("text.random", "Random effects model")
setOption("text.predict", "Prediction interval")
setOption("text.w.common", "common")
setOption("text.w.fixed", "common")
setOption("text.w.random", "random")
setOption("title", "")
setOption("complab", "")
setOption("CIbracket", "[")
setOption("CIseparator", "; ")
setOption("CIlower.blank", TRUE)
setOption("CIupper.blank", TRUE)
setOption("print.subgroup.name", TRUE)
setOption("print.byvar", TRUE)
setOption("sep.subgroup", " = ")
setOption("byseparator", " = ")
setOption("test.subgroup", TRUE)
setOption("prediction.subgroup", FALSE)
setOption("keepdata", TRUE)
setOption("keeprma", FALSE)
setOption("warn", TRUE)
setOption("warn.deprecated", TRUE)
setOption("transf", TRUE)
setOption("backtransf", TRUE)
setOption("digits", 4)
setOption("digits.mean", 2)
setOption("digits.sd", 4)
setOption("digits.se", 4)
setOption("digits.stat", 2)
setOption("digits.zval", 2)
setOption("digits.Q", 2)
setOption("digits.tau2", 4)
setOption("digits.tau", 4)
setOption("digits.H", 2)
setOption("digits.I2", 1)
setOption("digits.prop", 4)
setOption("digits.weight", 1)
setOption("digits.pval", 4)
setOption("digits.pval.Q", 4)
setOption("digits.df", 4)
setOption("scientific.pval", FALSE)
setOption("big.mark", "")
setOption("zero.pval", TRUE)
setOption("JAMA.pval", FALSE)
##
setOption("details", TRUE)
##
setOption("print.tau2", TRUE)
setOption("print.tau2.ci", TRUE)
setOption("print.tau", TRUE)
setOption("print.tau.ci", TRUE)
setOption("print.I2", TRUE)
setOption("print.I2.ci", TRUE)
setOption("print.H", TRUE)
setOption("print.Rb", FALSE)
setOption("text.tau2", "tau^2")
setOption("text.tau", "tau")
setOption("text.I2", "I^2")
setOption("text.Rb", "Rb")
##
setOption("print.Q", TRUE)
##
## Default summary measure
##
setOption("smbin", "RR")
setOption("smcont", "MD")
setOption("smcor", "ZCOR")
setOption("sminc", "IRR")
setOption("smmean", "MRAW")
setOption("smprop", "PLOGIT")
setOption("smrate", "IRLN")
##
## Settings for R functions metabin, metainc, metaprop
##
setOption("incr", 0.5)
setOption("method.incr", "only0")
setOption("allincr", FALSE)
setOption("addincr", FALSE)
##
## Additional settings for R function metabin
##
setOption("method", "MH")
setOption("allstudies", FALSE)
setOption("MH.exact", FALSE)
setOption("RR.Cochrane", FALSE)
setOption("Q.Cochrane", TRUE)
setOption("model.glmm", "UM.FS")
setOption("print.CMH", FALSE)
##
## Additional setting for R function metacont
##
setOption("pooledvar", FALSE)
setOption("method.smd", "Hedges")
setOption("sd.glass", "control")
setOption("exact.smd", TRUE)
setOption("method.ci.cont", "z")
##
## Additional setting for R function metaprop
##
setOption("method.ci.prop", "CP")
##
## Additional setting for R function metarate
##
setOption("method.ci.rate", "NAsm")
##
## Settings for R functions comparing two treatments
##
setOption("label.e", "Experimental")
setOption("label.c", "Control")
setOption("label.left", "")
setOption("label.right", "")
##
## Settings for R function forest.meta
##
setOption("layout", "meta")
setOption("forest.details", FALSE)
setOption("test.overall", FALSE)
setOption("test.effect.subgroup", FALSE)
setOption("digits.forest", 2)
setOption("digits.TE.forest", 4)
##
setOption("lty.common", 2)
setOption("lty.random", 3)
setOption("col.common", "black")
setOption("col.random", "black")
##
setOption("sort.subgroup", FALSE)
##
setOption("pooled.events", FALSE)
setOption("pooled.times", FALSE)
setOption("study.results", TRUE)
##
setOption("lower.equi", NA)
setOption("upper.equi", NA)
setOption("lty.equi", 1)
setOption("col.equi", "blue")
setOption("fill.equi", "transparent")
##
setOption("fill", "transparent")
##
setOption("leftcols", NULL)
setOption("rightcols", NULL)
setOption("leftlabs", NULL)
setOption("rightlabs", NULL)
##
setOption("label.e.attach", NULL)
setOption("label.c.attach", NULL)
##
setOption("bottom.lr", TRUE)
##
setOption("lab.NA", ".")
setOption("lab.NA.effect", NULL)
setOption("lab.NA.weight", ".")
##
setOption("lwd", 1)
setOption("lwd.square", 1)
setOption("lwd.diamond", 1)
##
setOption("arrow.type", "open")
setOption("arrow.length", 0.05)
##
setOption("type.study", "square")
setOption("type.common", "diamond")
##
setOption("col.study", "black")
setOption("col.square", "gray")
setOption("col.square.lines", "gray")
setOption("col.circle", "royalblue")
setOption("col.inside", "white")
setOption("col.diamond", "gray")
setOption("col.diamond.lines", "black")
setOption("col.predict", "red")
setOption("col.predict.lines", "black")
setOption("col.subgroup", "black")
setOption("col.label.right", "black")
setOption("col.label.left", "black")
##
setOption("col.lines", "black")
setOption("col.label", "black")
##
setOption("hetlab", "Heterogeneity: ")
setOption("resid.hetstat", NULL)
setOption("resid.hetlab", "Residual heterogeneity: ")
##
setOption("forest.I2", NULL)
setOption("forest.I2.ci", FALSE)
setOption("forest.tau2", NULL)
setOption("forest.tau2.ci", FALSE)
setOption("forest.tau", FALSE)
setOption("forest.tau.ci", FALSE)
setOption("forest.Q", FALSE)
setOption("forest.pval.Q", NULL)
setOption("forest.Rb", FALSE)
setOption("forest.Rb.ci", FALSE)
##
setOption("text.subgroup.nohet", "not applicable")
##
setOption("LRT", FALSE)
##
setOption("forest.stat", TRUE)
setOption("forest.Q.subgroup", TRUE)
##
setOption("header.line", FALSE)
##
setOption("fontsize", 12)
setOption("fontfamily", NULL)
setOption("fs.common", NULL)
setOption("fs.random", NULL)
setOption("fs.predict", NULL)
setOption("fs.common.labels", NULL)
setOption("fs.random.labels", NULL)
setOption("fs.predict.labels", NULL)
setOption("fs.hetstat", NULL)
setOption("fs.test.overall", NULL)
setOption("fs.test.subgroup", NULL)
setOption("fs.test.effect.subgroup", NULL)
setOption("fs.addline", NULL)
##
setOption("ff.heading", "bold")
setOption("ff.common", NULL)
setOption("ff.random", NULL)
setOption("ff.predict", NULL)
setOption("ff.common.labels", NULL)
setOption("ff.random.labels", NULL)
setOption("ff.predict.labels", NULL)
setOption("ff.study", "plain")
setOption("ff.hetstat", NULL)
setOption("ff.test.overall", NULL)
setOption("ff.test.subgroup", NULL)
setOption("ff.test.effect.subgroup", NULL)
setOption("ff.addline", NULL)
setOption("ff.axis", "plain")
setOption("ff.smlab", "bold")
setOption("ff.xlab", "plain")
setOption("ff.lr", "plain")
##
setOption("colgap", "2mm")
setOption("colgap.forest", "2mm")
##
setOption("width", NULL)
##
setOption("calcwidth.predict", FALSE)
setOption("calcwidth.hetstat", FALSE)
setOption("calcwidth.tests", FALSE)
setOption("calcwidth.subgroup", FALSE)
setOption("calcwidth.addline", FALSE)
##
setOption("just.studlab", "left")
setOption("just.addcols", "center")
##
setOption("spacing", 1)
setOption("addrow", NULL)
setOption("addrow.overall", NULL)
setOption("addrow.subgroups", NULL)
setOption("addrows.below.overall", NULL)
setOption("Wan2014.Table1",
c(0.000, 1.128, 1.693, 2.059, 2.326,
2.534, 2.704, 2.847, 2.970, 3.078,
3.173, 3.259, 3.336, 3.407, 3.472,
3.532, 3.588, 3.640, 3.689, 3.735,
3.778, 3.819, 3.858, 3.895, 3.931,
3.964, 3.997, 4.027, 4.057, 4.086,
4.113, 4.139, 4.165, 4.189, 4.213,
4.236, 4.259, 4.280, 4.301, 4.322,
4.341, 4.361, 4.379, 4.398, 4.415,
4.433, 4.450, 4.466, 4.482, 4.498))
##
setOption("Wan2014.Table2",
c(0.990, 1.144, 1.206, 1.239, 1.260,
1.274, 1.284, 1.292, 1.298, 1.303,
1.307, 1.311, 1.313, 1.316, 1.318,
1.320, 1.322, 1.323, 1.324, 1.326,
1.327, 1.328, 1.329, 1.330, 1.330,
1.331, 1.332, 1.332, 1.333, 1.333,
1.334, 1.334, 1.335, 1.335, 1.336,
1.336, 1.336, 1.337, 1.337, 1.337,
1.338, 1.338, 1.338, 1.338, 1.339,
1.339, 1.339, 1.339, 1.339, 1.340))
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Defines functions second setVar getVar setOption catobsev cathet condense collapse qdat hetdat taudat update_needed updateversion .onAttach
.onAttach <- function(libname, pkgname) {
msg <-
paste0("Loading 'meta' package (version ",
utils::packageDescription("meta")$Version,
").",
"\nType 'help(meta)' for a brief overview.")
packageStartupMessage(msg)
}
updateversion <- function(x) {
##
## Update older meta objects, see gs("major.update") and gs("minor.update")
##
if (update_needed(x$version))
x <- update(x, warn = FALSE, warn.deprecated = FALSE)
##
x
}
update_needed <- function(version,
major = gs("major.update"),
minor = gs("minor.update"),
verbose = FALSE) {
if (is.null(version)) {
version <- 0.1
major.cur <- 0
minor.cur <- 1
}
else {
version <- unlist(strsplit(version, "-"))
divide <- unlist(strsplit(version[1], ".", fixed = TRUE))
major.cur <- as.numeric(divide[1])
minor.cur <- as.numeric(paste(divide[2], version[2], sep = "."))
}
##
res <-
ifelse(major.cur < major,
TRUE, ifelse(major.cur > major,
FALSE, minor.cur < as.numeric(gsub("-", ".", minor))))
if (res & verbose)
message(paste0("Update to meta, version ", major, ".", minor))
##
res
}
taudat <- function(method.tau, detail.tau,
tau, lower.tau, upper.tau, print.tau.ci, digits.tau,
tau2, lower.tau2, upper.tau2, print.tau2.ci, digits.tau2,
sign.lower, sign.upper) {
dat <- data.frame(method.tau, names = detail.tau, tau, tau2)
##
## In order to use duplicated()
##
if (!is.null(dat$tau))
dat$tau <- round(dat$tau, 14)
if (!is.null(dat$tau2))
dat$tau2 <- round(dat$tau2, 14)
##
if (!is.null(lower.tau))
dat$lower.tau <- round(lower.tau, 14)
if (!is.null(lower.tau2))
dat$lower.tau2 <- round(lower.tau2, 14)
##
if (!is.null(upper.tau))
dat$upper.tau <- round(upper.tau, 14)
if (!is.null(upper.tau2))
dat$upper.tau2 <- round(upper.tau2, 14)
##
if (!is.null(sign.lower))
dat$sign.lower <- sign.lower
if (!is.null(sign.upper))
dat$sign.upper <- sign.upper
##
if (!is.null(names(tau)))
dat$names <- names(tau)
##
sel1 <- !duplicated(dat[, c("method.tau", "tau", "tau2")])
##
if (!is.null(dat$lower.tau) & !is.null(dat$lower.tau2) &
!is.null(dat$upper.tau) & !is.null(dat$upper.tau2))
sel2 <- !duplicated(dat[, c("method.tau", "tau", "tau2",
"lower.tau", "upper.tau",
"lower.tau2", "upper.tau2")])
else
sel2 <- sel1
##
sel <- sel1 & sel2
##
dat <- dat[sel, , drop = FALSE]
##
if (print.tau.ci) {
dat$lower.tau <- round(dat$lower.tau, digits.tau)
dat$upper.tau <- round(dat$upper.tau, digits.tau)
}
##
if (print.tau2.ci) {
dat$lower.tau2 <- round(dat$lower.tau2, digits.tau2)
dat$upper.tau2 <- round(dat$upper.tau2, digits.tau2)
}
dat
}
hetdat <- function(I2, lowI2, uppI2, print.I2, print.I2.ci, digits.I2,
H, lowH, uppH, print.H, digits.H,
Rb, lowRb, uppRb, print.Rb) {
dat <- data.frame()
##
if (print.I2) {
if (nrow(dat) == 0)
dat <- data.frame(I2 = round(I2, digits.I2))
else
dat$I2 <- round(I2, digits.I2)
##
if (print.I2.ci) {
dat$lowI2 <- round(lowI2, digits.I2)
dat$uppI2 <- round(uppI2, digits.I2)
}
}
##
if (print.H) {
if (nrow(dat) == 0)
dat <- data.frame(H = round(H, digits.H))
else
dat$H <- round(H, digits.H)
##
if (print.I2.ci) {
dat$lowH <- round(lowH, digits.H)
dat$uppH <- round(uppH, digits.H)
}
}
##
if (print.Rb) {
if (nrow(dat) == 0)
dat <- data.frame(Rb = round(Rb, digits.I2))
else
dat$Rb <- round(Rb, digits.I2)
##
if (print.I2.ci) {
dat$lowRb <- round(lowRb, digits.I2)
dat$uppRb <- round(uppRb, digits.I2)
}
}
##
if (!is.null(names(I2)))
dat$names <- names(I2)
else if (!is.null(names(H)))
dat$names <- names(H)
else if (!is.null(names(Rb)))
dat$names <- names(Rb)
##
dat <- unique(dat)
dat
}
qdat <- function(Q, df.Q, pval.Q, hetlabel, text.common) {
if (length(Q) > 1) {
if (!is.null(names(Q)))
rownames.Q <- names(Q)
else if (!is.null(hetlabel) && length(hetlabel) == length(Q))
rownames.Q <- hetlabel
else if (length(text.common) == length(Q))
rownames.Q <- text.common
else
rownames.Q <- rep("", length(Q))
}
else
rownames.Q <- rep("", length(Q))
##
sel <- rownames.Q != ""
rownames.Q[sel] <- paste0(" ", rownames.Q[sel])
##
dat <- data.frame(Q, df.Q, pval.Q, names = rownames.Q)
dat <- unique(dat)
dat
}
collapse <- function(x, quote = '"', collapse = ", ", sort = FALSE)
paste0(paste0(quote, if (sort) sort(x) else x, quote, collapse = collapse))
condense <- function(x, var)
unlist(lapply(x, "[[" , var))
cathet <- function(k,
method.tau, detail.tau,
tau2, lower.tau2, upper.tau2,
print.tau2, print.tau2.ci, text.tau2, digits.tau2,
tau, lower.tau, upper.tau,
print.tau, print.tau.ci, text.tau, digits.tau,
sign.lower.tau, sign.upper.tau,
I2, lowI2, uppI2,
print.I2, print.I2.ci, text.I2, digits.I2,
H, lowH, uppH,
print.H, digits.H,
Rb, lowRb, uppRb,
print.Rb, text.Rb,
big.mark,
sort.tau = NULL, sort.het = NULL) {
if (is.null(lower.tau2))
lower.tau2 <- NA
if (is.null(upper.tau2))
upper.tau2 <- NA
if (is.null(lower.tau))
lower.tau <- NA
if (is.null(upper.tau))
upper.tau <- NA
##
if (all(is.na(lower.tau2) & is.na(upper.tau2)))
print.tau2.ci <- FALSE
if (all(is.na(lower.tau) & all(is.na(upper.tau))))
print.tau.ci <- FALSE
## Text for tau2 and tau
##
dtau <- taudat(method.tau, detail.tau,
tau, lower.tau, upper.tau, print.tau.ci, digits.tau,
tau2, lower.tau2, upper.tau2, print.tau2.ci, digits.tau2,
sign.lower.tau, sign.upper.tau)
##
ntau <- nrow(dtau)
sort.tau <- setsort(sort.tau, ntau, "tau2 estimates")
dtau <- dtau[sort.tau, , drop = FALSE]
##
if (print.tau2 | print.tau) {
if (ntau > 1) {
text.tau2 <- paste(text.tau2, seq_len(ntau), sep = ".")
text.tau <- paste(text.tau, seq_len(ntau), sep = ".")
}
}
##
label.tau <-
if (ntau > 1)
ifelse(dtau$names == "", "", paste0(" (", dtau$names, ")"))
else
""
##
if (print.tau2.ci) {
text.tau2.ci <-
pasteCI(dtau$lower.tau2, dtau$upper.tau2,
digits.tau2, big.mark,
dtau$sign.lower, dtau$sign.upper)
text.tau2.ci[text.tau2.ci == " "] <- ""
}
else
text.tau2.ci <- ""
##
if (print.tau.ci) {
text.tau.ci <-
pasteCI(dtau$lower.tau, dtau$upper.tau,
digits.tau, big.mark,
dtau$sign.lower, dtau$sign.upper)
text.tau.ci[text.tau.ci == " "] <- ""
}
else
text.tau.ci <- ""
##
hettxt <-
paste0(
if (print.tau2 | print.tau | print.I2 | print.H | print.Rb)
" ",
if (print.tau2)
paste0(formatPT(dtau$tau2,
lab = TRUE, labval = text.tau2,
digits = digits.tau2,
lab.NA = "NA",
big.mark = big.mark),
text.tau2.ci,
if (!print.tau) label.tau),
##
if (print.tau)
paste0(
if (print.tau2) "; " else "",
formatPT(dtau$tau,
lab = TRUE, labval = text.tau,
digits = digits.tau,
lab.NA = "NA",
big.mark = big.mark),
text.tau.ci,
label.tau),
collapse = "\n")
## Text for I2, H and Rb
##
dhet <- hetdat(I2, lowI2, uppI2, print.I2, print.I2.ci, digits.I2,
H, lowH, uppH, print.H, digits.H,
Rb, lowRb, uppRb, print.Rb)
##
nhet <- nrow(dhet)
sort.het <- setsort(sort.het, nhet, "heterogeneity estimates")
dhet <- dhet[sort.het, , drop = FALSE]
##
label.het <-
if (nhet > 1)
ifelse(dhet$names == "", "", paste0(" (", dhet$names, ")"))
else
""
##
if (print.I2) {
if (nhet > 1)
text.I2 <- paste(text.I2, seq_len(nhet), sep = ".")
}
##
if (print.H) {
text.H <- "H"
if (nhet > 1)
text.H <- paste(text.H, seq_len(nhet), sep = ".")
}
##
if (print.Rb) {
if (nhet > 1)
text.Rb <- paste(text.Rb, seq_len(nhet), sep = ".")
}
##
if (print.I2)
hettxt <-
paste0(hettxt,
ifelse(print.tau2 | print.tau,
ifelse(ntau > 1 | print.tau2.ci | print.tau.ci |
(options()$width < 70 & print.I2.ci),
"\n", ";"),
""))
##
hettxt <-
paste0(hettxt,
paste0(
if (print.I2)
paste0(
if (print.tau2 | print.tau)
" ",
text.I2, " = ",
ifelse(is.na(dhet$I2), "NA",
paste0(formatN(dhet$I2, digits.I2), "%")),
if (print.I2.ci)
pasteCI(dhet$lowI2, dhet$uppI2, digits.I2,
big.mark, unit = "%"),
if (nhet > 1 & !print.H)
label.het
),
##
if (print.H)
paste0(
if (print.tau2 | print.tau | print.I2)
"; " else " ",
text.H, " = ",
ifelse(is.na(dhet$H), "NA",
formatN(dhet$H, digits.H, "NA", big.mark = big.mark)),
if (print.I2.ci & any(!is.na(lowH) & !is.na(uppH)))
pasteCI(dhet$lowH, dhet$uppH, digits.H, big.mark),
if (nhet > 1)
label.het),
collapse = "\n")
)
##
if (print.Rb)
hettxt <-
paste0(hettxt,
ifelse(print.tau2 | print.tau | print.I2 | print.H,
ifelse(ntau > 1 | nhet > 1 |
print.tau2.ci | print.tau.ci |
print.I2.ci |
(options()$width < 70 & print.I2.ci),
"\n", ";"),
""))
##
if (print.Rb)
hettxt <-
paste0(hettxt,
paste0(
" ",
text.Rb, " = ",
ifelse(is.na(dhet$Rb), "NA",
paste0(formatN(dhet$Rb, digits.I2,
big.mark = big.mark), "%")),
if (any(!is.na(dhet$lowRb) & !is.na(dhet$uppRb)))
pasteCI(dhet$lowRb, dhet$uppRb, digits.I2,
big.mark, unit = "%"),
label.het,
collapse = "\n")
)
## Remove spaces before ";", " (" and a line break
##
hettxt <- gsub("(*UCP)\\s+(;)", "\\1", hettxt, perl = TRUE)
hettxt <- gsub("(*UCP)\\s+( \\()", "\\1", hettxt, perl = TRUE)
hettxt <- gsub("(*UCP)\\s+(\\\n)", "\\1", hettxt, perl = TRUE)
## Print information on heterogeneity
##
cat(hettxt)
## Empty row(s)
##
if (print.tau2 | print.tau | print.I2 | print.H | print.Rb)
cat("\n")
invisible(NULL)
}
catobsev <- function(var1, var2 = NULL, type = "n", addrow = FALSE,
big.mark = gs("big.mark")) {
if (type == "n") {
txt <- "observations"
idx <- "o"
}
else if (type == "e") {
txt <- "events"
idx <- "e"
}
##
if (!is.null(var1) & !is.null(var2)) {
if (!(all(is.na(var1)) | all(is.na(var2)))) {
sum1 <- sum(var1, na.rm = TRUE)
sum2 <- sum(var2, na.rm = TRUE)
##
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum1 + sum2, big.mark = big.mark),
if (type == "n")
paste0(" (", idx, ".e = ",
format(sum1, big.mark = big.mark),
", ", idx, ".c = ",
format(sum2, big.mark = big.mark),
")"),
"\n"))
}
}
else if (!is.null(var1)) {
if (!all(is.na(var1))) {
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum(var1, na.rm = TRUE),
big.mark = big.mark),
"\n"))
}
}
else if (!is.null(var2)) {
if (!all(is.na(var2))) {
cat(paste0("Number of ", txt, ": ", idx, " = ",
format(sum(var2, na.rm = TRUE), big.mark = big.mark),
"\n"))
}
}
##
if (addrow)
cat("\n")
##
invisible(NULL)
}
## The following R code is based on the file snowfall-internal.R from
## R package snowfall (Maintainer: Jochen Knaus <jo@imbi.uni-freiburg.de>)
##
## Helpers for managing the internal variables in the package namespace without
## awake the R CMD check for later R versions (which basically blaims many
## global assignments).
##
## The given solution has an advantage: only writing is affected. Reading of the
## objects can remain the same (thanks to Uwe Ligges for the tipp):
## reading: gs("CIbracket")
## writing: setOption("CIbracket", "(")
##
##
## Set an option in the meta option list.
## (Basically this is the setting of a list entry).
## key - character: object name
## val - object (everything is allowed, even NULL)
##
setOption <- function(key = NULL, val = NULL) {
if(!is.null(key) && is.character(key)) {
option <- getVar(".settings") # Get from NS
option[[key]] <- val
setVar(".settings", option) # Write to NS
##
return(invisible(TRUE))
}
##
stop("Argument 'key' or 'val' is NULL or 'key' is no string.")
}
##
## Get a specific variable from the meta namespace.
## var - character: object name
##
getVar <- function(var = NULL) {
if(!is.null(var) && is.character(var)) {
tmp <- try(getFromNamespace(var, "meta"))
##
if(inherits(tmp, "try-error"))
stop("Object", var, "not found in meta package.")
##
return(tmp)
}
stop("Argument 'var' is NULL or not a string.")
}
##
## Write a specific variable to the meta namespace.
## var - character: object name
## arg - object (NULL allowed)
##
setVar <- function(var = NULL, arg = NULL) {
if(!is.null(var) && is.character(var)) {
assignInNamespace(var, arg, "meta")
return(invisible(TRUE))
}
stop("var is NULL or no character");
}
second <- function(x) x[2]
.settings <- list()
##
## List of internal settings
##
argslist.internal <-
c("Wan2014.Table1", "Wan2014.Table2",
"sm4bin", "sm4cont", "sm4cor", "sm4inc", "sm4mean", "sm4prop", "sm4rate",
"ci4cont", "ci4prop", "ci4rate",
"meth4bin", "meth4inc", "meth4prop", "meth4rate",
"meth4tau", "meth4tau.ci", "meth4i2",
"meth4random.ci", "meth4pi",
"adhoc4hakn.ci", "adhoc4hakn.pi",
"meth4bias", "meth4bias.old",
"tool4rob",
"meth4incr",
"text.fixed", "text.w.fixed",
"major.update", "minor.update",
#
"special.characters")
##
setOption("argslist.internal", argslist.internal)
##
## Set defaults (for internal options)
##
setOption("sm4bin", c("OR", "RD", "RR", "ASD", "DOR", "VE"))
setOption("sm4cont", c("MD", "SMD", "ROM"))
setOption("sm4cor", c("ZCOR", "COR"))
setOption("sm4inc", c("IRR", "IRD", "IRSD", "VE"))
setOption("sm4mean", c("MRAW", "MLN"))
setOption("sm4prop", c("PLOGIT", "PLN", "PRAW", "PAS", "PFT"))
setOption("sm4rate", c("IR", "IRLN", "IRS", "IRFT"))
##
setOption("ci4cont", c("z", "t"))
setOption("ci4prop", c("CP", "WS", "WSCC", "AC", "SA", "SACC", "NAsm"))
setOption("ci4rate", c("NAsm", "Poisson"))
##
setOption("meth4bin", c("Inverse", "MH", "Peto", "GLMM", "LRP", "SSW"))
setOption("meth4inc", c("Inverse", "MH", "Cochran", "GLMM"))
setOption("meth4prop", c("Inverse", "GLMM"))
setOption("meth4rate", c("Inverse", "GLMM"))
##
setOption("meth4tau", c("DL", "PM", "REML", "ML", "HS", "SJ", "HE", "EB"))
setOption("meth4tau.ci", c("QP", "BJ", "J", "PL", ""))
setOption("meth4i2", c("Q", "tau2"))
setOption("meth4random.ci", c("classic", "HK", "KR"))
setOption("meth4pi",
c("V", "HTS", "HK", "HK-PR", "KR", "KR-PR", "NNF", "S", ""))
setOption("adhoc4hakn.ci", c("", "se", "ci", "IQWiG6"))
setOption("adhoc4hakn.pi", c("", "se"))
##
setOption("meth4bias.old", c("rank", "linreg", "mm", "count", "score"))
setOption("meth4bias", c("Begg", "Egger", "Thompson", "Schwarzer",
"Harbord", "Peters", "Deeks",
"Pustejovsky", "Macaskill"))
##
setOption("tool4rob",
c("RoB1", "RoB2", "RoB2-cluster", "RoB2-crossover",
"ROBINS-I", "ROBINS-E"))
##
setOption("meth4incr", c("only0", "if0all", "all"))
#
setOption("special.characters", c("+", ".", "&", "$", "#", "|", "*", "^"))
#
setOption("major.update", 5)
setOption("minor.update", 6)
##
## List of arguments that can be changed by user
##
argslist <-
c("level", "level.ma", "common", "random",
"method.random.ci", "method.predict",
"adhoc.hakn.ci", "adhoc.hakn.pi",
"method.tau", "method.tau.ci", "level.hetstat", "tau.common",
"method.I2",
"prediction", "level.predict",
"method.bias",
"tool.rob",
"overall.hetstat",
"text.common", "text.random", "text.predict",
"text.w.common", "text.w.random",
"title", "complab",
"CIbracket", "CIseparator", "CIlower.blank", "CIupper.blank",
"print.subgroup.name", "sep.subgroup",
"keepdata", "keeprma", "warn", "warn.deprecated",
"transf", "backtransf",
"smbin", "smcont", "smcor", "sminc", "smmean", "smprop", "smrate",
"incr", "method.incr",
"method", "allstudies", "MH.exact",
"RR.Cochrane", "Q.Cochrane", "model.glmm", "print.CMH",
"pooledvar", "method.smd", "sd.glass", "exact.smd",
"method.ci.cont", "method.ci.prop", "method.ci.rate",
"label.e", "label.c", "label.left", "label.right",
"layout", "forest.details",
"test.overall", "test.subgroup", "prediction.subgroup",
"test.effect.subgroup",
"digits", "digits.mean", "digits.sd", "digits.se", "digits.stat",
"digits.Q", "digits.tau2", "digits.tau", "digits.H", "digits.I2",
"digits.prop", "digits.weight",
"digits.pval", "digits.pval.Q",
"digits.forest", "digits.TE.forest",
"digits.df",
"scientific.pval", "big.mark", "zero.pval", "JAMA.pval",
"details",
"print.tau2", "print.tau2.ci", "print.tau", "print.tau.ci",
"print.I2", "print.I2.ci", "print.H", "print.Rb",
"text.tau2", "text.tau", "text.I2", "text.Rb",
"print.Q",
##
"lty.common", "lty.random", "col.common", "col.random",
"sort.subgroup",
"pooled.events", "pooled.times", "study.results",
"lower.equi", "upper.equi", "lty.equi", "col.equi", "fill.equi",
"fill",
"leftcols", "rightcols", "leftlabs", "rightlabs",
"label.e.attach", "label.c.attach",
"bottom.lr",
"lab.NA", "lab.NA.effect", "lab.NA.weight",
"lwd", "lwd.square", "lwd.diamond",
"arrow.type", "arrow.length",
"type.study", "type.common",
"col.study", "col.square", "col.square.lines", "col.circle", "col.inside",
"col.diamond", "col.diamond.lines",
"col.predict", "col.predict.lines",
"col.subgroup",
"col.label.right", "col.label.left",
"col.lines", "col.label",
"hetlab", "resid.hetstat", "resid.hetlab",
"forest.I2", "forest.I2.ci", "forest.tau2", "forest.tau2.ci",
"forest.tau", "forest.tau.ci", "forest.Q", "forest.pval.Q",
"forest.Rb", "forest.Rb.ci",
"text.subgroup.nohet",
"LRT",
"forest.stat", "forest.Q.subgroup",
"header.line",
"fontsize", "fontfamily",
"fs.common", "fs.random", "fs.predict",
"fs.common.labels", "fs.random.labels", "fs.predict.labels",
"fs.hetstat", "fs.test.overall", "fs.test.subgroup",
"fs.test.effect.subgroup", "fs.addline",
"ff.heading", "ff.common", "ff.random", "ff.predict",
"ff.common.labels", "ff.random.labels", "ff.predict.labels",
"ff.study", "ff.hetstat", "ff.test.overall", "ff.test.subgroup",
"ff.test.effect.subgroup", "ff.addline",
"ff.axis", "ff.smlab", "ff.xlab", "ff.lr",
"colgap", "colgap.forest",
"width",
"calcwidth.predict", "calcwidth.hetstat",
"calcwidth.tests", "calcwidth.subgroup", "calcwidth.addline",
"just.studlab", "just.addcols",
"spacing",
"addrow", "addrow.overall", "addrow.subgroups", "addrows.below.overall"
)
#
args.depr <- c("fixed", "comb.fixed", "comb.random", "level.comb",
"hakn", "adhoc.hakn",
"digits.zval", "print.byvar", "byseparator",
"addincr", "allincr")
#
setOption("argslist", c(argslist, args.depr))
#
setOption("argslist.meta", c(argslist, args.depr))
##
## General settings
##
setOption("level", 0.95)
setOption("level.ma", 0.95)
setOption("level.comb", 0.95)
##
setOption("common", TRUE)
setOption("fixed", TRUE)
setOption("comb.fixed", TRUE)
setOption("random", TRUE)
setOption("comb.random", TRUE)
setOption("method.random.ci", "classic")
setOption("hakn", FALSE)
setOption("adhoc.hakn", "")
setOption("adhoc.hakn.ci", "")
setOption("adhoc.hakn.pi", "")
setOption("prediction", FALSE)
setOption("level.predict", 0.95)
setOption("method.predict", "V")
setOption("method.tau", "REML")
setOption("method.tau.ci", NULL)
setOption("level.hetstat", 0.95)
setOption("tau.common", FALSE)
setOption("method.I2", "Q")
setOption("method.bias", "Egger")
setOption("tool.rob", NULL)
setOption("overall.hetstat", NULL)
setOption("text.common", "Common effect model")
setOption("text.fixed", "Common effect model")
setOption("text.random", "Random effects model")
setOption("text.predict", "Prediction interval")
setOption("text.w.common", "common")
setOption("text.w.fixed", "common")
setOption("text.w.random", "random")
setOption("title", "")
setOption("complab", "")
setOption("CIbracket", "[")
setOption("CIseparator", "; ")
setOption("CIlower.blank", TRUE)
setOption("CIupper.blank", TRUE)
setOption("print.subgroup.name", TRUE)
setOption("print.byvar", TRUE)
setOption("sep.subgroup", " = ")
setOption("byseparator", " = ")
setOption("test.subgroup", TRUE)
setOption("prediction.subgroup", FALSE)
setOption("keepdata", TRUE)
setOption("keeprma", FALSE)
setOption("warn", TRUE)
setOption("warn.deprecated", TRUE)
setOption("transf", TRUE)
setOption("backtransf", TRUE)
setOption("digits", 4)
setOption("digits.mean", 2)
setOption("digits.sd", 4)
setOption("digits.se", 4)
setOption("digits.stat", 2)
setOption("digits.zval", 2)
setOption("digits.Q", 2)
setOption("digits.tau2", 4)
setOption("digits.tau", 4)
setOption("digits.H", 2)
setOption("digits.I2", 1)
setOption("digits.prop", 4)
setOption("digits.weight", 1)
setOption("digits.pval", 4)
setOption("digits.pval.Q", 4)
setOption("digits.df", 4)
setOption("scientific.pval", FALSE)
setOption("big.mark", "")
setOption("zero.pval", TRUE)
setOption("JAMA.pval", FALSE)
##
setOption("details", TRUE)
##
setOption("print.tau2", TRUE)
setOption("print.tau2.ci", TRUE)
setOption("print.tau", TRUE)
setOption("print.tau.ci", TRUE)
setOption("print.I2", TRUE)
setOption("print.I2.ci", TRUE)
setOption("print.H", TRUE)
setOption("print.Rb", FALSE)
setOption("text.tau2", "tau^2")
setOption("text.tau", "tau")
setOption("text.I2", "I^2")
setOption("text.Rb", "Rb")
##
setOption("print.Q", TRUE)
##
## Default summary measure
##
setOption("smbin", "RR")
setOption("smcont", "MD")
setOption("smcor", "ZCOR")
setOption("sminc", "IRR")
setOption("smmean", "MRAW")
setOption("smprop", "PLOGIT")
setOption("smrate", "IRLN")
##
## Settings for R functions metabin, metainc, metaprop
##
setOption("incr", 0.5)
setOption("method.incr", "only0")
setOption("allincr", FALSE)
setOption("addincr", FALSE)
##
## Additional settings for R function metabin
##
setOption("method", "MH")
setOption("allstudies", FALSE)
setOption("MH.exact", FALSE)
setOption("RR.Cochrane", FALSE)
setOption("Q.Cochrane", TRUE)
setOption("model.glmm", "UM.FS")
setOption("print.CMH", FALSE)
##
## Additional setting for R function metacont
##
setOption("pooledvar", FALSE)
setOption("method.smd", "Hedges")
setOption("sd.glass", "control")
setOption("exact.smd", TRUE)
setOption("method.ci.cont", "z")
##
## Additional setting for R function metaprop
##
setOption("method.ci.prop", "CP")
##
## Additional setting for R function metarate
##
setOption("method.ci.rate", "NAsm")
##
## Settings for R functions comparing two treatments
##
setOption("label.e", "Experimental")
setOption("label.c", "Control")
setOption("label.left", "")
setOption("label.right", "")
##
## Settings for R function forest.meta
##
setOption("layout", "meta")
setOption("forest.details", FALSE)
setOption("test.overall", FALSE)
setOption("test.effect.subgroup", FALSE)
setOption("digits.forest", 2)
setOption("digits.TE.forest", 4)
##
setOption("lty.common", 2)
setOption("lty.random", 3)
setOption("col.common", "black")
setOption("col.random", "black")
##
setOption("sort.subgroup", FALSE)
##
setOption("pooled.events", FALSE)
setOption("pooled.times", FALSE)
setOption("study.results", TRUE)
##
setOption("lower.equi", NA)
setOption("upper.equi", NA)
setOption("lty.equi", 1)
setOption("col.equi", "blue")
setOption("fill.equi", "transparent")
##
setOption("fill", "transparent")
##
setOption("leftcols", NULL)
setOption("rightcols", NULL)
setOption("leftlabs", NULL)
setOption("rightlabs", NULL)
##
setOption("label.e.attach", NULL)
setOption("label.c.attach", NULL)
##
setOption("bottom.lr", TRUE)
##
setOption("lab.NA", ".")
setOption("lab.NA.effect", NULL)
setOption("lab.NA.weight", ".")
##
setOption("lwd", 1)
setOption("lwd.square", 1)
setOption("lwd.diamond", 1)
##
setOption("arrow.type", "open")
setOption("arrow.length", 0.05)
##
setOption("type.study", "square")
setOption("type.common", "diamond")
##
setOption("col.study", "black")
setOption("col.square", "gray")
setOption("col.square.lines", "gray")
setOption("col.circle", "royalblue")
setOption("col.inside", "white")
setOption("col.diamond", "gray")
setOption("col.diamond.lines", "black")
setOption("col.predict", "red")
setOption("col.predict.lines", "black")
setOption("col.subgroup", "black")
setOption("col.label.right", "black")
setOption("col.label.left", "black")
##
setOption("col.lines", "black")
setOption("col.label", "black")
##
setOption("hetlab", "Heterogeneity: ")
setOption("resid.hetstat", NULL)
setOption("resid.hetlab", "Residual heterogeneity: ")
##
setOption("forest.I2", NULL)
setOption("forest.I2.ci", FALSE)
setOption("forest.tau2", NULL)
setOption("forest.tau2.ci", FALSE)
setOption("forest.tau", FALSE)
setOption("forest.tau.ci", FALSE)
setOption("forest.Q", FALSE)
setOption("forest.pval.Q", NULL)
setOption("forest.Rb", FALSE)
setOption("forest.Rb.ci", FALSE)
##
setOption("text.subgroup.nohet", "not applicable")
##
setOption("LRT", FALSE)
##
setOption("forest.stat", TRUE)
setOption("forest.Q.subgroup", TRUE)
##
setOption("header.line", FALSE)
##
setOption("fontsize", 12)
setOption("fontfamily", NULL)
setOption("fs.common", NULL)
setOption("fs.random", NULL)
setOption("fs.predict", NULL)
setOption("fs.common.labels", NULL)
setOption("fs.random.labels", NULL)
setOption("fs.predict.labels", NULL)
setOption("fs.hetstat", NULL)
setOption("fs.test.overall", NULL)
setOption("fs.test.subgroup", NULL)
setOption("fs.test.effect.subgroup", NULL)
setOption("fs.addline", NULL)
##
setOption("ff.heading", "bold")
setOption("ff.common", NULL)
setOption("ff.random", NULL)
setOption("ff.predict", NULL)
setOption("ff.common.labels", NULL)
setOption("ff.random.labels", NULL)
setOption("ff.predict.labels", NULL)
setOption("ff.study", "plain")
setOption("ff.hetstat", NULL)
setOption("ff.test.overall", NULL)
setOption("ff.test.subgroup", NULL)
setOption("ff.test.effect.subgroup", NULL)
setOption("ff.addline", NULL)
setOption("ff.axis", "plain")
setOption("ff.smlab", "bold")
setOption("ff.xlab", "plain")
setOption("ff.lr", "plain")
##
setOption("colgap", "2mm")
setOption("colgap.forest", "2mm")
##
setOption("width", NULL)
##
setOption("calcwidth.predict", FALSE)
setOption("calcwidth.hetstat", FALSE)
setOption("calcwidth.tests", FALSE)
setOption("calcwidth.subgroup", FALSE)
setOption("calcwidth.addline", FALSE)
##
setOption("just.studlab", "left")
setOption("just.addcols", "center")
##
setOption("spacing", 1)
setOption("addrow", NULL)
setOption("addrow.overall", NULL)
setOption("addrow.subgroups", NULL)
setOption("addrows.below.overall", NULL)
setOption("Wan2014.Table1",
c(0.000, 1.128, 1.693, 2.059, 2.326,
2.534, 2.704, 2.847, 2.970, 3.078,
3.173, 3.259, 3.336, 3.407, 3.472,
3.532, 3.588, 3.640, 3.689, 3.735,
3.778, 3.819, 3.858, 3.895, 3.931,
3.964, 3.997, 4.027, 4.057, 4.086,
4.113, 4.139, 4.165, 4.189, 4.213,
4.236, 4.259, 4.280, 4.301, 4.322,
4.341, 4.361, 4.379, 4.398, 4.415,
4.433, 4.450, 4.466, 4.482, 4.498))
##
setOption("Wan2014.Table2",
c(0.990, 1.144, 1.206, 1.239, 1.260,
1.274, 1.284, 1.292, 1.298, 1.303,
1.307, 1.311, 1.313, 1.316, 1.318,
1.320, 1.322, 1.323, 1.324, 1.326,
1.327, 1.328, 1.329, 1.330, 1.330,
1.331, 1.332, 1.332, 1.333, 1.333,
1.334, 1.334, 1.335, 1.335, 1.336,
1.336, 1.336, 1.337, 1.337, 1.337,
1.338, 1.338, 1.338, 1.338, 1.339,
1.339, 1.339, 1.339, 1.339, 1.340))
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